Research workbench
Crystal structure of VAT(D) in complex with virginiamycin and coenzyme a
Analyse Crystal structure of VAT(D) in complex with virginiamycin and coenzyme a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KHR
- Type
- protein
- Length
- 1,233 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Streptogramin a acetyltransferase
- EC
- 2.3.1.-
- UniProt
- P50870
- Ligands
- COA, VIR
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Streptogramin a acetyltransferase (EC 2.3.1.-) | protein | 206 | 26% helix, 20% strand | P50870 |
| B | Streptogramin a acetyltransferase (EC 2.3.1.-) | protein | 205 | 24% helix, 21% strand | P50870 |
| E | Streptogramin a acetyltransferase (EC 2.3.1.-) | protein | 204 | 25% helix, 21% strand | P50870 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
- VIR · Virginiamycin M1 · ligand · 3 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.72 | 0.80 | 56 | COA, VIR |
| 2 | 544 | 0.72 | 0.80 | 56 | VIR, COA |
| 3 | 558 | 0.71 | 0.80 | 57 | COA |
| 4 | 571 | 0.71 | 0.79 | 60 | VIR, COA |
| 5 | 596 | 0.71 | 0.79 | 60 | COA |
Interfaces
6 interfaces between chains.
- A–B · 1349 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1335 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1334 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1321 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1321 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1KHR · Crystal Structure of Vat(D) in Complex with Virginiamycin and Coenzyme A · the same entry in another collection · chain D against D, TM-score 1.00
- P50870 · AlphaFold monomer V2.0 prediction for streptogramin a acetyltransferase (P50870) · a predicted model of the same protein · chain E against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P50870
- Elsewhere: RCSB PDB 1KHR · PDBe 1KHR · UniProt P50870
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